2YN2 | pdb_00002yn2

Huf protein - paralogue of the tau55 histidine phosphatase domain

• PDB DOI: https://doi.org/10.2210/pdb2YN2/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-11 Released: 2013-04-03 
• Deposition Author(s): Taylor, N.M.I., Glatt, S., Hennrich, M., von Scheven, G., Grotsch, H., Fernandez-Tornero, C., Rybin, V., Gavin, A.C., Kolb, P., Muller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.236 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Characterization of a Phosphatase Domain within Yeast General Transcription Factor Tfiiic.

Taylor, N.M.I., Glatt, S., Hennrich, M.L., Von Scheven, G., Grotsch, H., Fernandez-Tornero, C., Rybin, V., Gavin, A., Kolb, P., Muller, C.W.

(2013) J Biological Chem 288: 15110

• PubMed: 23569204 
• DOI: https://doi.org/10.1074/jbc.M112.427856
• Primary Citation Related Structures: 
  2YN0, 2YN2


• PubMed Abstract: 
  

  Saccharomyces cerevisiae τ55, a subunit of the RNA polymerase III-specific general transcription factor TFIIIC, comprises an N-terminal histidine phosphatase domain (τ55-HPD) whose catalytic activity and cellular function is poorly understood. We solved the crystal structures of τ55-HPD and its closely related paralogue Huf and used in silico docking methods to identify phosphoserine- and phosphotyrosine-containing peptides as possible substrates that were subsequently validated using in vitro phosphatase assays. A comparative phosphoproteomic study identified additional phosphopeptides as possible targets that show the involvement of these two phosphatases in the regulation of a variety of cellular functions. Our results identify τ55-HPD and Huf as bona fide protein phosphatases, characterize their substrate specificities, and provide a small set of regulated phosphosite targets in vivo.

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Organizational Affiliation: 
• Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.02 kDa 
• Atom Count: 2,156 
• Modeled Residue Count: 254 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNCHARACTERIZED PROTEIN YNL108C	A	279	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53929 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53929  Go to UniProtKB:  P53929

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.236 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.72	α = 90
b = 86.72	β = 90
c = 98.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Taylor, N.M.I., Glatt, S., Hennrich, M., von Scheven, G., Grotsch, H., Fernandez-Tornero, C., Rybin, V., Gavin, A.C., Kolb, P., Muller, C.W.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-04-17
  Changes: Database references
• Version 1.2: 2013-04-24
  Changes: Structure summary
• Version 1.3: 2013-06-12
  Changes: Database references
• Version 2.0: 2023-12-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description